Project Summary Chronic viral infections are major causes of chronic inflammation and cancer. A well characterized example is virus-induced liver disease and hepatocellular carcinoma, the second leading cause of death world-wide. Using virus-induced liver disease and cancer as a model, we aim to develop sophisticated computational tools to investigate the host cell reprogramming induced by viruses during cancerogenesis. Leveraging and enhancing advanced computational approaches, we will develop an integrative genomic framework to identify the regulatory modules driving transcriptional and proteomic reprogramming associated with persistent viral infection and carcinogenesis. More specifically, we will develop a toolbox that allows for inferring regulatory mechanisms from time course data derived from different viral infections associated with similar disease biology and multiple functional genomics levels in an integrated manner. We hypothesize that the computational toolbox developed within this program will contribute to understand viral carcinogenesis and identify novel strategies for cancer prevention.